Rice fields are major source of atmospheric methane (CH₄). However, 30%~90% of CH₄produced in paddy soils is oxidized by methanotrophs before it escapes to the atmosphere. China holds the largest rice production in the world, but it remains largely unknown about the active methane oxidizers in paddy soils. In this study, soil microcosms of six paddy soil incubated with ¹³CH₄ were constructed to assess active methanotrophs by tracing the isotopically labeled ¹³C-DNA/RNA. Six paddy soils collected from Yingtan City of Jiangxi Province (YT), Ziyang City of Sichuan Province (ZY), Jiaxing City of Zhejiang Province (JX), Changshu City of Jiangsu Province (CS), Yangzhou City of Jiangsu Province (YZ), and Wuchang City of Heilongjiang Province (WC), were incubated with 400 µmol^-1 L labeled ¹³CH₄ or unlabeled ¹²CH₄ to determine aerobic methane oxidation kinetics. The destructive sampling was conducted when 400 µmol^-1 L CH₄ was consumed. ¹³C-DNA and ¹³C-RNA were obtained through ultracentrifugation of total DNA and RNA, respectively. Clone library of pmoA genes from ¹³C-DNA and 16S rRNA genes from ¹³C-RNA were constructed to analyze composition of active methanotrophic community. After ultracentrifugation of total DNA and RNA, the agarose gel electrophoresis of pmoA gene amplicons and methanotrophic 16S rRNA reverse transcription amplicons from the fractionated DNA and rRNA, respectively, were performed, indicating the incorporation of ¹³C-substrate into methanotrophs during the aerobic methane oxidation. DNA-SIP and rRNA-SIP each have their advantages. In contrast to DNA, the incorporation of labeled substrate into rRNA is much faster, and a greater unspecific background of ‘heavy’ nucleic acid was observed in ‘heavy’ fractions in rRNA-SIP than DNA-SIP, indicating the more efficient separation for DNA. The separation of differentially labeled rRNA was effective, however, it was not as quantitative as for DNA. This resulted in a greater unspecific background of ‘heavy’ rRNA in ‘light’ fractions, which may be caused by their strong tendency to form secondary structure. Phylogenetic analysis of pmoA gene from total DNA of background paddy soils indicated that dominant methanotrophs in situ were type II in six paddy soils. It may be explained by the fact that type II methanotrohs can be better adapted to oligotrophic environments. Interestingly, consistent results were obtained from both clone libraries of pmoA genes from ¹³C-DNA and methanotrophic 16S rRNA transcripts from ¹³C-RNA, indicating that type I methanotrophs dominated active aerobic methane oxidation in the six paddy soils. All type I was composed of type Ia in YT and WC sample, whereas type I was composed of Ia and Ib in ZY, JX, CS and JD sample. The fast growth found for type I methanotrophs are in agree with a r-strategy lifestyle. Sufficient available nutrient e.g. CH4 may be prerequisite for the proliferation of type I methanotrophs. Phylogenetic analysis of pmoA gene from ¹³C-DNA and 16S rRNA transcript from ¹³C-rRNA revealed that the active methanotrophs responsible for aerobic methane oxidation in six paddy soils were type I. The results indicated that methanotroph-specific 16S rRNA and pmoA genes can be of great help for identification of ¹³C-DNA/RNA from methanotrophs grown on the labeled substrates.